title: SCCVII_tumor_3_S3

city: La Jolla

first: Judith

middle: Anne

last: Varner

address: Center for Novel Therapeutics 9310 Athena Circle 9310 Athena Circle

department: Pathology

institute: University of California, San Diego

description:
One biological replicate of in vitro cultured HPV negative SSCVII tumor cells
HNSCC_all_genes_results.txt
3_SCCVII_tumor_3_S3

data_processing:
Base calling used Illumina's  Real-Time Analysis software called RTA2
Quality assessment used FASTQC, then mapped to mm10 whole genome using STAR 2.5.3a.
Quantification used RSEM 1.3.0. Annotation used Mus_musculus.GRCm38.68.gtf.
MultiQC was used to aggregate QC results into a single report
Genome_build: Mus musculus GRCm38-mm10 was used as reference sequence for alignment
Supplementary_files_format_and_content: tab-delimited text files include gene count, TPM, and FPKM values for each Sample.

source_name: SSCVII  in vitro cultured tumor cells

growth_protocol: Murine macrophages were sorted from implanted head and neck tumors using flow sorting for CD45+CD11b+ Gr1-F4/80hi cell populations. 3 replicate samples, each pooled from 3- 4 replicate mice were sequenced per tumor model: HPV+MEER, HPV-MEER and SSCVII. 3 replicate aliquots of tumor cell lines were also sequenced (HPV+MEER, HPV-MEER and SSCVII). Additionally, triplicate preparations of macrophage colonies derived from these sorted macrophages were also sequenced.

extract_protocol:
RNA was purified from each fresh cell sample using Qiagen Rneasy kits. RNA quality and concentration was evaluated using Agilent Tape Station prior to library construction.
RNA libraries were prepared using Ilumina TruSeq Stranded mRNA protocols

treatment_protocol: Macrophages were sorted from dissociated tumors using flow cytometry  for  CD45+CD11b+ Gr1-F4/80hi populations, and RNA was isloated. Macrophage colony cell RNA was isolated from cultures of macrophages plated in Stem Cell Technologies hematopoietic stem cell medium (SCM) for 9 days. Tumor cell RNA was isolated from in vitro cultured tumor cells.

tag: tumor  origin

value: HPV-SSCVII

value: tumor cell


title: SCCVII_tumor_1_S1

status: Public on Nov 06 2019

type: SRA

state: CA

country: USA

description:
One biological replicate of in vitro cultured HPV negative SSCVII tumor cells
HNSCC_all_genes_results.txt
1_SCCVII_tumor_1_S1

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type


title: SCCVII_macrophage_2_S5

description:
One biological replicate preparation of Gr1-F4/80hi macrophages isolated from HPV negative SSCVII tumors from C3H/HeJ mice
HNSCC_all_genes_results.txt
5_SCCVII_macrophage_2_S5

source_name: CD45+CD11b+Gr1-F4/80hi macrophages sorted from subcutaneous SSCVII  tumors

value: macrophage


title: SCCVII_macrophage_1_S4

description:
One biological replicate preparation of  Gr1-F4/80hi macrophages isolated from HPV negative SSCVII tumors from C3H/HeJ mice
HNSCC_all_genes_results.txt
4_SCCVII_macrophage_1_S4


title: SCCVII_macrophage_3_S6

description:
One biological replicate preparation of  Gr1-F4/80hi macrophages isolated from HPV negative SSCVII tumors from C3H/HeJ mice
HNSCC_all_genes_results.txt
6_SCCVII_macrophage_3_S6


title: SCCVII_colony_1_S7

description:
One biological replicate preparation of In vitro cultured macrophage progenitor colonies derived from Gr1-F4/80hi macrophages isolated from HPV negative SSCVII tumors from C3H/HeJ mice
HNSCC_all_genes_results.txt
7_SCCVII_colony_1_S7

source_name: Colony cells derived form CD45+CD11b+Gr1-F4/80hi macrophages sorted from subcutaneous HPV- SSCVII tumors

value: macrophage progenitor colony


title: HPV.positive_tumor_3_S16

description:
One biological replicate preparation of in vitro cultured HPV positive MEER tumor cells
HNSCC_all_genes_results.txt
21_HPV-positive_tumor_3_S16

source_name: HPV+ MEER  in vitro cultured tumor cells

value: HPV+ MEER


title: SCCVII_colony_2_S8

description:
One biological replicate preparation of In vitro cultured macrophage progenitor colonies derived from Gr1-F4/80hi macrophages isolated from HPV negative SSCVII tumors from C3H/HeJ mice
HNSCC_all_genes_results.txt
8_SCCVII_colony_2_S8


title: HPV.positive_tumor_2_S15

description:
One biological replicate preparation of in vitro cultured HPV positive MEER tumor cells
HNSCC_all_genes_results.txt
20_HPV-positive_tumor_2_S15


title: HPV.positive_tumor_1_S14

description:
One biological replicate preparation of in vitro cultured HPV positive MEER tumor cells
HNSCC_all_genes_results.txt
19_HPV-positive_tumor_1_S14


title: HPV.positive_macrophage_2_S18

description:
One biological replicate preparation of Gr1-F4/80hi macrophages isolated from HPV positive MEER tumors from Bl6 mice
HNSCC_all_genes_results.txt
23_HPV-positive_macrophage_2_S18

source_name: CD45+CD11b+Gr1-F4/80hi macrophages sorted from subcutaneous HPV+ MEER tumors


title: HPV.positive_macrophage_3_S19

description:
One biological replicate preparation of Gr1-F4/80hi macrophages isolated from HPV positive MEER tumors from Bl6 mice
HNSCC_all_genes_results.txt
24_HPV-positive_macrophage_3_S19


title: SW480_EVR2_RNASeq

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

description:
empty vector replicate 2 (Stranded)
SW480-KD_raw_counts.txt

data_processing:
Quality of sequencing reads assessed with FastQC (v0.11.5).
An index of the hg38 genome was created, and reads were aligned with STAR (v2.6.1a) with the additional parameter --outSAMtype BAM SortedByCoordinate.
Coordinated sorted BAM files were indexed with Samtools (v1.9).
Reads were assigned to the nearest gene and counted using Rsubread (v1.24.2) with the additional parameters: isGTFAnnotationFile=TRUE GTF.featureType='exon' GTF.attrType='gene_id' useMetaFeatures=TRUE allowMultiOverlap=FALSE minOverlap=5 countMultiMappingReads=TRUE isPairedEnd=FALSE and either strandSpecific=2 or strandSpecific=0 depending on whether the library preparation was strand specific or not.
EdgeR (v3.24.0) was used for differential expression analysis. Genes with CPM expression less than 0.5 in more than one sample replicate were excluded from the model.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts

organism: Homo sapiens

source_name: SW480 Cells

extract_protocol:
Cells were collected by scraping prior to total RNA isolation using RNeasy mini kit (Qiagen, 74104).
Libraries were generated using Illumina TruSeq Stranded mRNA (Illumina, 20020594).

tag: genotype

value: empty vector


title: HPV.positive_macrophage_1_S17

description:
One biological replicate preparation of Gr1-F4/80hi macrophages isolated from HPV positive MEER tumors from Bl6 mice
HNSCC_all_genes_results.txt
22_HPV-positive_macrophage_1_S17


title: Clone10GFPneg_1

city: New York

first: Kelly

middle: Madigan

last: Banks

state: NY

address: 1300 York Ave, LC711

department: Surgery

institute: Weill Cornell Medicine

description: RNA seq

data_processing:
Raw reads were aligned using STAR v2.3.0e_r291
Read counting was performed using htseq-count v0.6.0
Differential gene expression analysis using DeSeq2
Gene enrichment analysis using GSEA
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: DeSeq results

source_name: mESC

growth_protocol: mESCs were cultured in KO DMEM, 1% GlutaMAX, 1x Pen-Strep. 1x NEAA, 0.1 mM 2-Mercaptoethanol, 1000 units/ml rmLIF, and 15% Serum

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
Libraries prepared using IlluminaTruSeq RNA Sample Preparation Kits v2

treatment_protocol: 6 uM (Z)-4-Hydroxytamoxifen for 48 hours

value: GFP- Sphk1fl/fl Sphk2-/-

tag: passage


title: HPV.negative_tumor_2_S10

description:
One biological replicate preparation of in vitro cultured HPV negative MEER tumor cells
HNSCC_all_genes_results.txt
11_HPV-negative_tumor_2_S10

source_name: HPV- MEER  in vitro cultured tumor cells

value: HPV- MEER


title: HPV.negative_tumor_1_S9

description:
One biological replicate preparation of in vitro cultured HPV negative MEER tumor cells
HNSCC_all_genes_results.txt
10_HPV-negative_tumor_1_S9


title: HPV.negative_macrophage_4_S20

description:
One biological replicate preparation ofGr1-F4/80hi macrophages isolated from HPV negative MEER tumors from Bl6 mice
HNSCC_all_genes_results.txt
25_HPV-negative_macrophage_4_S20

source_name: CD45+CD11b+Gr1-F4/80hi macrophages sorted from subcutaneous HPV- MEER tumors


title: HPV.negative_macrophage_2_S13

description:
One biological replicate preparation ofGr1-F4/80hi macrophages isolated from HPV negative MEER tumors from Bl6 mice
HNSCC_all_genes_results.txt
14_HPV-negative_macrophage_2_S13


title: HPV.negative_macrophage_1_S12

description:
One biological replicate preparation of Gr1-F4/80hi macrophages isolated from HPV negative MEER tumors from Bl6 mice
HNSCC_all_genes_results.txt
13_HPV-negative_macrophage_1_S12


title: Clone4GFPpos_1

description: RNA seq

value: GFP+ Sphk1-/- Sphk2-/-


title: HPV.negative_colony_3_S3

description:
One biological replicate preparation of In vitro cultured macrophage progenitor colonies derived from Gr1-F4/80hi macrophages isolated from HPV negative MEER tumors from Bl6 mice
HNSCC_all_genes_results2.txt
3_HPV-negative_colony_3_S3

source_name: Colony cells derived from CD45+CD11b+Gr1-F4/80hi macrophages sorted from subcutaneous HPV- MEER tumors


title: KO_ST rep3

city: Seoul

first: Joonhong

last: Kwon

address: 84, Heukseok-ro, Dongjak-gu

country: South Korea

institute: Chung-Ang University

data_processing:
Basecall performed using Phred base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT v2.1.0 which handles spliced read mapping through the Bowtie2 aligner  2.3.4.1, to generate aligned reads
StringTie 1.3.4d used for transcript assembly
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) by expression quantification got from the transcript quantification of each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
Brains were removed and sectioned PFC (prefrontal cortex) region. RNA was harvested using miRNeasy mini kit (Qiagen, 217004). Illumina Truseq Standed mRNA LT Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: prefrontal cortex

tag: age

tag: treatment

value: stressed


title: KO_ST rep1


title: WT_ST rep2

value: wild type


title: WT_ST rep1


title: WT_ST rep3


title: CT rep3

value: control


title: CT rep2


title: CT rep1


title: HPV.negative_tumor_3_S11

description:
One biological replicate preparation of in vitro cultured HPV negative MEER tumor cells
HNSCC_all_genes_results.txt
12_HPV-negative_tumor_3_S11


title: epiKSMO3_mCherry_E9.5_embryo1

first: Sergiy

last: Velychko

state: MA

address: 77 Avenue Louis Pasteur, Room 232

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were aligned to the mm10 reference genome using CLC Genomics Workbench 11.0.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include TPM values for each sample (cut off=1).

molecule: polyA RNA

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated as described previously (Takahashi and Yamanaka, 2006). MEFs and HEK 293T cells were cultured in low-glucose DMEM supplemented with 10% FBS (Ch), 1% Glutamax, 1% penicillin-streptomycin, 1% nonessential amino acids (NEAA), 0.5% β-mercaptoethanol (all from Life Technologies). Mouse embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) were grown on irradiated C3H MEFs in high-glucose DMEM medium (Life Technologies) supplemented with 15% KSR, 2% FCS, 1% Glutamax, 1% NEAA, 1% penicillin-streptomycin, 1% β-mercaptoethanol, and 20 ng/ml human recombinant LIF (purified in-house). The cells were routinely tested for Mycoplasma contamination. Tetraploid complementation was performed as described before (Russell et al., 2015). Briefly, two-cell–stage embryos were fused with electrical pulses. The fused embryos (tetraploid, 4N) were cultured for 24 hrs to the 4-cell stage and aggregated with fifteen trypsin-digested iPSCs. The aggregates were cultured at 37C, 5% CO2 for 24 h and subsequently transferred into one uterine horn of a 2.5 dpc pseudopregnant recipient CD-1 mice for full term development.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN)
NEBNExt ultra Directional RNA Kit with polyA enrichment was used for library preparation.

treatment_protocol: Reprogramming: OG2 MEFs or heterozygous ROSA26-rtTA/GOF18 MEFs of passage 3 or 4 were split on 12-well plates (3x104 per well). Simultaneously, the cells were infected with virus-containing supernatant supplemented with 6 µg/ml protamine sulphate (Sigma-Aldrich). 30 µl of non-concentrated tetO-SKM virus and 30 µl of rtTA virus (in the case of OG2 MEFs) were added to 1 ml of fresh medium. The volumes of the rest of the viruses were adjusted accordingly to Q-PCR titration. The cells were washed and medium was replaced with dox-containing (1 µg/ml unless otherwise mentioned) embryonic stem cell medium (high-glucose DMEM with LIF) 48 hours after infection. Alternatively, the infected cells were passaged on inactivated C3H feeders and next day induced with Dox. The number of GFP+ colonies were counted 1 and 2 weeks after Dox induction. Dox was removed after 12 days of induction (2 days before the second evaluation) to count only transgene-independent iPSC colonies. For the RNAi experiment, OG2 MEFs were infected with pLKO.puro shRNA viruses and selected with (8μg/ml) puromycin. After 48 hours, the cells were split and infected with rtTA and tetO-OSKM or tetO-SKM viruses as described above. The selection with (4μg/ml) puromycin was continued during the whole reprogramming experiment to eliminate the cells that silence shRNA transgenes. Statistical significance was calculated using Student's t-test.

value: EF1alpha-mCherry-sorted iPSC-derived differentiated cells at E9.5


title: OSKM3_mCherry_E9.5_embryo3

source_name: sorted iPSC-derived differentiated cells at E9.5


title: OSKM2_mCherry_E9.5_embryo1


title: epiKSMO2_mCherry_E9.5_embryo3


title: OSKM2_mCherry_E9.5_embryo3


title: SKM1_mCherry_E9.5_embryo3


title: OSKM3_mCherry_E9.5_embryo2


title: SKM1_mCherry_E9.5_embryo2


title: OSKM2_mCherry_E9.5_embryo2


title: OSKM3_mCherry_E9.5_embryo1


title: SKM1_mCherry_E9.5_embryo1


title: epiKSMO3_mCherry_E9.5_embryo3


title: epiKSMO1_mCherry_E9.5_embryo2


title: epiKSMO1_mCherry_E9.5_embryo3


title: epiKSMO2_mCherry_E9.5_embryo1


title: epiKSMO2_mCherry_E9.5_embryo2


title: HPV.negative_colony_2_S2

description:
One biological replicate preparation of In vitro cultured macrophage progenitor colonies derived from Gr1-F4/80hi macrophages isolated from HPV negative MEER tumors from Bl6 mice
HNSCC_all_genes_results2.txt
2_HPV-negative_colony_2_S2


title: epiKSMO1_mCherry_E9.5_embryo1


title: HPV.negative_colony_1_S1

description:
One biological replicate preparation of In vitro cultured macrophage progenitor colonies derived from Gr1-F4/80hi macrophages isolated from HPV negative MEER tumors from Bl6 mice
HNSCC_all_genes_results2.txt
1_HPV-negative_colony_1_S1


title: KO_ST rep2


title: epiKSM1_mCherry_E9.5_embryo3


title: SCCVII_tumor_2_S2

description:
One biological replicate of in vitro cultured HPV negative SSCVII tumor cells
HNSCC_all_genes_results.txt
2_SCCVII_tumor_2_S2


title: epiKSM1_mCherry_E9.5_embryo2


title: epiKSM1_mCherry_E9.5_embryo1


title: Control_E9.5_embryo3

source_name: Embryo at E9.5

value: Embryo at E9.5, mock-sorted


title: Control_E9.5_embryo2


title: epiKSMO3_mCherry_E9.5_embryo2


title: SKM3_68.2

source_name: induced Pluripotent Stem Cell line

value: tet-inducible lentivirus-derived induced Pluripotent Stem Cell line, the number indicated efficiency in 4N complementation assay


title: SKM5_13.9


title: OSKM4_7.7


title: SKM1_78.8


title: OSKM5_0


title: RNAseq_IMR90_CAPH2_KD3

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq: 76-bp or 50-bp reads were aligned to the human genome (hg19) using Bowtie2 (version 2.2.9).
ChIP-seq: Redundant reads were removed by picard (version 2.7.1). Low quality read (MapQ < 10) were also removed.
ChIP-seq: peaks were defined by HOMER software (version 4.8.3) using the option “-center -style factor -F 1 -P 0.0001 -fdr 0.05” for RNA Pol II and TP53, while the alternative option “-center -style histone -F 2 -P 0.0001 -fdr 0.05” was used for other proteins. Input samples were used for the control of peak calling.
ChIP-seq: score of more than 7-fold compared to the Input were removed from the bigwig file.
Supplementary_files_format_and_content: ChIP-seq: bigwig file were generated using bedGraphToBigWig (version 4)
RNA-seq: Sequenced reads were aligned to the human genome (hg19) using the STAR program (v2.5.2)
RNA-seq: Reads assigned to exons were estimated by the RSEM program (v1.2.31) ), and genes carrying less than 10 reads were eliminated, resulting in total 19,591 genes.
RNA-seq: Read numbers in different samples were normalized using the DEseq2 program ver3.7
RNA-seq: The DEseq2 program was used to identify differently expressed genes. CAP-H2 KD samples (KD#1 and KD#3) were treated as biological replicas. FDR < 0.05 was used as a threshold to identify significantly up- or down-regulated genes.
Supplementary_files_format_and_content: ChIP-seq: bigwig file were generated using bedGraphToBigWig (version 4)
Supplementary_files_format_and_content: RNA-seq: tab-deliminated text files of ensemble gene ID and expected read count obtained from RSEM calculation.

source_name: IMR90 cells

growth_protocol: Normal diploid IMR90 human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.15% sodium bicarbonate, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1 ´ MEM non-essential amino acids. BJ human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
In situ Hi-C was performed as previously described (Rao et al., 2014, Cell). ChIP-seq was performed as previously described (Aird et al., 2017 JCB).  RNA was extracted from IMR90 cells using RNeasy Mini kit (Qiagen).  RNA-seq was carried out as previously described with modifications (Tanizawa et al. 2017 NSMB).
For in situ Hi-C, sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc). ChIP-seq was carried out as described previously (Iwasaki et al. 2015).  Approximately 1 ng ChIP DNA was subjected to the illumine library construction using NEBNext Ultra DNA library prep kit (New England Biolabs).  Adaptor-ligated DNA was PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.  For RNA-seq, Poly (A) RNA was purified using NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs), and sequence libraries were constructed using NEBNext mRNA Library prep Master mix for Illumina (New England Biolabs).  Adaptor-ligated DNAs were PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.

treatment_protocol: pBABE-puro plasmids carrying H-rasV12 were used for retrovirus packaging, and virus infection was performed.  H-rasV12-expressing cells were cultured in medium containing 1 µg/ml puromycin for 7 days to obtain OIS cells. pTRIPZ plasmids containing NCAPH2 shRNAs (#1, V3THS_326285; #2, V3THS_326286; #3, V3THS_326290, Dharmacon) were used for CAP-H2 knockdown.  Lentivirus was prepared using ViraPower kit (Thermo Fisher Scientifc) according to the manufacturer’s protocol.  Doxycycline (1μg/ml) was added to culture medium every 48 hours after lentiviral transfection for shRNA expression. OIS cells were further infected with lentivirus encoding one of the three shRNA constructs (#1, #2, and #3) against NCAPH2 and harvested 3 days after the lentivirus infection.

tag: cell line

value: Lung fibroblasts

tag: genotype/variation

value: CAP-H2 knockdown

tag: cell status

value: OIS (Oncogene-Induced Senescence) cells

tag: karyotype

value: Normal diploid


title: Control_E9.5_embryo1


title: SKM4_9.3


title: SKM2_59.1


title: RNAseq_IMR90_CAPH2_KD2

data_processing:
ChIP-seq: 76-bp or 50-bp reads were aligned to the human genome (hg19) using Bowtie2 (version 2.2.9).
ChIP-seq: Redundant reads were removed by picard (version 2.7.1). Low quality read (MapQ < 10) were also removed.
ChIP-seq peaks were defined by HOMER software (version 4.8.3) using the option “-center -style factor -F 1 -P 0.0001 -fdr 0.05” for RNA Pol II and TP53, while the alternative option “-center -style histone -F 2 -P 0.0001 -fdr 0.05” was used for other proteins. Input samples were used for the control of peak calling.
ChIP-seq score of more than 7-fold compared to the Input were removed from the bigwig file.
Supplementary_files_format_and_content: ChIP-seq: bigwig file were generated using bedGraphToBigWig (version 4)
RNA-seq: Sequenced reads were aligned to the human genome (hg19) using the STAR program (v2.5.2)
RNA-seq: Reads assigned to exons were estimated by the RSEM program (v1.2.31) ), and genes carrying less than 10 reads were eliminated, resulting in total 19,591 genes.
RNA-seq: Read numbers in different samples were normalized using the DEseq2 program ver3.7
RNA-seq: The DEseq2 program was used to identify differently expressed genes. CAP-H2 KD samples (KD#1 and KD#3) were treated as biological replicas. FDR < 0.05 was used as a threshold to identify significantly up- or down-regulated genes.
Supplementary_files_format_and_content: ChIP-seq: bigwig file were generated using bedGraphToBigWig (version 4)
Supplementary_files_format_and_content: RNA-seq: tab-deliminated text files of ensemble gene ID and expected read count obtained from RSEM calculation.


title: RNAseq_IMR90_CAPH2_KD1


title: RNAseq_IMR90_OIS_control

value: wild type/control


title: RNAseq_IMR90_G

value: growing cells


title: KSM1_44.2


title: KSM2_56.3


title: ESC2_35

source_name: Embryonic Stem Cell line

value: Embryonic Stem Cell line, the number indicated efficiency in 4N complementation assay


title: KSM3_12


title: ESC1_73.3


title: ESC4_0


title: OSKM3_1.8


title: OSKM1_2.2


title: RNAseq_IMR90_OIS


title: epiKSMO2_63

value: episomally-derived induced Pluripotent Stem Cell line, the number indicated efficiency in 4N complementation assay


title: epiKSMO3_0


title: ESC3_0


title: OSKM2_0


title: ChIPseq_IMR90_SMC1_OIS

description: Validated by western blot

library_source: genomic

molecule: genomic DNA

value: Rabbit polyclonal anti-SMC1 (Bethyl Laboratories, A300-055A, lot# A4)


title: ChIPseq_IMR90_SMC1_G

description: Validated by western blot


title: epiKSMO1_0


title: epiKSM3_27


title: ChIPseq_IMR90_CTCF_G

description: Validated by western blot

value: Rabbit polyclonal anti-CTCF (Millipore, 07-729, lot# 2475698)


title: d12_SKM_GFP_Rep1

source_name: Reprogramming intermediates

value: Reprogramming intermediates, pMX-mCherry-negative, Oct4-GFP-positive


title: d12_SKM_GFP_Rep2


title: epiKSM2_30


title: epiKSM1_45


title: d12_OSKM_GFP_Rep2


title: d12_OSKM_GFP_Rep1


title: ChIPseq_IMR90_CAPH2_Bethyl276_OIS

description: Validated by RNAi & western blot

value: Rabbit polyclonal anti-CAP-H2 (Bethyl Laboratories, A302-276A, lot #A1)


title: ChIPseq_IMR90_CAPH2_Bethyl276_G

description: Validated by RNAi & western blot

value: wild type


title: ChIPseq_IMR90_CAPH2_FLAG_OIS1

description: Validated by RNAi & western blot

value: Mouse monoclonal anti-FLAG (clone M2, Sigma Aldrich),


title: ChIPseq_IMR90_CAPH2_FLAG_OIS2

description: Validated by RNAi & western blot


title: d9_SKM_GFP_Rep1


title: d9_SKM_GFP_Rep2


title: ChIPseq_IMR90_CAPH2_Bethyl275_G

description: Validated by RNAi & western blot

value: Rabbit polyclonal anti-CAP-H2 (Bethyl Laboratories, A302-275A, lot #A2)


title: ChIPseq_IMR90_CAPH2_Bethyl275_OIS2

description: Validated by RNAi & western blot


title: d6_OSKM_Epcam_Rep2

value: Reprogramming intermediates, pMX-mCherry-negative, Oct4-GFP-negative, Epcam-positive


title: d6_SKM_Epcam_Rep2


title: d9_OSKM_GFP_Rep2


title: d6_SKM_Epcam_Rep1


title: d9_OSKM_GFP_Rep1


title: ChIPseq_IMR90_CAPH2_FLAG_G

description: Validated by RNAi & western blot


title: InsituHiC_BJ_RS_Bio2

data_processing:
76-bp paired reads were separately aligned to the human genome (hg19) using Bowtie2 (version 2.2.9) with iterative alignment strategy.
Redundant paired reads derived from a PCR bias, reads aligned to repetitive sequences, and reads with low mapping quality (MapQ < 30) were removed.
Contact matrices were generated at three resolutions such as 10, 40, 200 kb. The entire human genome was divided into 10, 40, 200 kb sections. A raw contact matrix was first constructed by counting paired reads assigned to two genomic sections. Note that reads belong to MboI fragments.
Reads potentially derived from self-ligation and undigested products were also discarded.
Hi-C biases in contact maps were corrected using the ICE method. The ICE normalization was repeated 30 times.
Genome_build: hg19
Supplementary_files_format_and_content: tab-deliminated text files of normalized scores. First row and column indicate the location of the genome in following format, "<chromosome name>:<start position>:<end position>"

source_name: BJ cells

extract_protocol:
In situ Hi-C was performed as previously described (Rao et al., 2014, Cell)
Sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc).

value: Foreskin fibroblasts


title: InsituHiC_BJ_RS_Bio3


title: InsituHiC_BJ_RS_Bio1


title: d6_OSKM_Epcam_Rep1


title: ChIPseq_IMR90_CAPH2_Bethyl275_OIS1

description: Validated by RNAi & western blot

value: Lung fibroblasts


title: InsituHiC_BJ_G_Bio2


title: InsituHiC_BJ_G_Bio1


title: NLS Parkin hypoxia 3

city: San Diego

first: Justin

middle: Michael

last: Quiles

state: California

address: 9500 Gilman Drive

department: Skaggs School of Pharmacy & Pharmaceutical Sciences

institute: University of California San Diego

data_processing:
Quality control of the raw fastq files was performed using the software took FastQC v0.11.3.
Sequencing reads were trimmed with Trimmomatic v0.36  and aligned to the human genome (GRCh37.p13) using the STAR aligner v2.5.3a. Read quantification was performed with RSEM v 1.3.0 and the Gencode release 19.
The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis. In brief, lowly expressed genes (counts per million (cpm) >/= 1 in at least 4 of the samples), and then trimmed mean of M-values (TMM) normalization was applied. The values weighted for inter-subject correlations in repeated measures of samples, after which ImFit was used to fit per-gene linear models and empirical Bayes moderation was applied with the eBayes function.
Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing correction using a moderated t-statistic in limma and a minimum absolute log-fold-change threshold of 1.5.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: csv file contains counts for all genes across all 18 samples

source_name: HeLa_NLS Parkin hypoxia

growth_protocol: HeLa cells were plated and maintained in Dulbecco’s modified Eagle’s medium (DMEM, ThermoFisher) containing 10% fetal bovine serum (FBS, ThermoFisher) and antibiotics (100 U/mL penicillin and 100 µg/mL streptomycin).

extract_protocol:
RNA was isolated from cells using the RNeasy Mini Kit (Qiagen) following the manufacturers protocols.
RNA sequencing libraries were generated from 1 ug of total RNA using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following manufacturer’s instructions, modifying the shear time to 5 minutes. RNA libraries were multiplexed and sequenced with 75 basepair (bp) single reads (SR75) to a depth of approximately 25 million reads per sample on an Illumina HiSeq4000.

treatment_protocol: Cells were infected with adenoviral constructs for 3hr. Growth media was replaced and cells were grown in normoxic or hypoxic conditions for 12hrs. For hypoxia experiments, cells were cultured in media supplemented with 20mM HEPES pH 7.4 (ThermoFisher) and placed into BD GasPak EZ pouches (BD Biosciences).

value: HeLa

value: infected with adenovirus encoding mCherry-tagged nuclear-localized Parkin (NLS)

value: hypoxia (12hr)


title: ChIPseq_IMR90_CTCF_OIS

description: Validated by western blot

value: OIS (Oncogene-Induced Senescence) cells

value: Normal diploid


title: NLS Parkin hypoxia 2


title: InsituHiC_IMR90_RS_Bio1


title: mCherry hypoxia 2

source_name: HeLa_mCherry hypoxia

value: infected with adenovirus encoding mCherry alone


title: NLS Parkin hypoxia 1


title: Parkin hypoxia 1

source_name: HeLa_Parkin hypoxia

value: infected with adenovirus encoding mCherry-tagged wild-type Parkin


title: InsituHiC_IMR90_OIS_CAPH2_KD2


title: mCherry hypoxia 3


title: Parkin hypoxia 2


title: Parkin hypoxia 3


title: InsituHiC_IMR90_OIS_Bio2


title: InsituHiC_IMR90_OIS_CAPH2_KD3


title: NLS Parkin normoxia 3

source_name: HeLa_NLS Parkin normoxia

value: normoxia


title: L40_sucr_inib_14d_repl2

city: Pieve Emanuele-Milan

first: Giulia

last: Solda'

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

description:
Series 3
Rep2
Rep2_inib_14 day culture
CPM_TABLE_L40.txt

data_processing:
Reads were adapter-trimmed according to the Illumina pipeline (Bcl2fastq)
Reads were mapped to the human hg19 genome and transcripts using STAR 2.5 (PMID: 23104886)
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using DeSeq2 (PMID: 25516281 )
Genome_build: hg19 (GRCh37), transcripts from Homo Sapiens RefSeq
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance measurements (count per million reads, CPM)

source_name: Primary skin fibroblasts

growth_protocol: Skin fibroblasts from healthy subjects (L40, L37, and F1) were recovered according to ethical and legal recommendations. Fibroblasts were cultured in RPMI-1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: 500 ng of total RNA was subjected to library synthesis using the Illumina TruSeq Stranded mRNA Sample LS Preparation kit. 500 ng of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes. Sequencing was performed on a 2x75 paired end High flow cell.

treatment_protocol: Sucrose loading: fibroblasts cells were cultured for 2 or 14 days in complete growth medium supplemented with 88 mM sucrose. β-glucosidases inhibition: after 12 days of sucrose loading, fibroblasts were treated for 48 hours with Conduritol B epoxide (CBE) at 0.5 mM and Adamantane–pentyl-dNM;N-(5-adamantane-1-yl-methoxy-pentyl)-Deoxynojirimycin (AMP-DNM) at 20 nM.

tag: donor

value: fibroblast

value: sucrose+AMP+DNM

tag: time

value: 14 day culture


title: InsituHiC_IMR90_OIS_Bio1


title: InsituHiC_IMR90_G_Bio1


title: InsituHiC_IMR90_OIS_Bio3


title: NLS Parkin normoxia 2


title: InsituHiC_IMR90_OIS_CAPH2_KD1


title: Parkin normoxia 1

source_name: HeLa_Parkin normoxia


title: mCherry normoxia 3

source_name: HeLa_mCherry normoxia


title: Parkin normoxia 2


title: InsituHiC_IMR90_RS_Bio2


title: NLS Parkin normoxia 1


title: InsituHiC_IMR90_OIS_CAPH2_KD4


title: mCherry normoxia 2


title: L40_sucr_inib_14d_repl1

description:
Series 3
Rep1
Rep1_inib_14 day culture
CPM_TABLE_L40.txt


title: L40_sucr_inib_14d_repl3

description:
Series 3
Rep3
Rep3_inib_14 day culture
CPM_TABLE_L40.txt


title: L40_sucr_2d_repl3

description:
Series 2
Rep3
Rep3_sucr_2 day culture
CPM_TABLE_L40.txt

value: sucrose

value: 2 day culture


title: mCherry hypoxia 1


title: Parkin normoxia 3


title: InsituHiC_IMR90_G_Bio2


title: L40_sucr_2d_repl1

description:
Series 2
Rep1
Rep1_sucr_2 day culture
CPM_TABLE_L40.txt


title: L40_UT_2d_repl2

description:
Series 2
Rep2
Rep2_ctr_2 day culture
CPM_TABLE_L40.txt

value: untreated


title: L40_UT_2d_repl3

description:
Series 2
Rep3
Rep3_ctr_2 day culture
CPM_TABLE_L40.txt


title: L40_UT_2d_repl1

description:
Series 2
Rep1
Rep1_ctr_2 day culture
CPM_TABLE_L40.txt


title: mCherry normoxia 1


title: L40_sucr_14d_repl3

description:
Series 1
Rep3
Rep3_sucr_L40
Rep3_sucr_14 day culture
CPM_TABLE_14d_3lines.txt
CPM_TABLE_L40.txt


title: 2: LPS 40 mg/kg 1.5h

type: RNA

city: Budapest

first: Pál

last: Tod

state: Budapest

address: Szigony utca 43

country: Hungary

institute: Institute of Experimental Medicine

description: Biological replicate 4 of 4. 40 mg/kg LPS, harvest at 1.5 hours

hyb_protocol: Hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria)

scan_protocol: Scanned on Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)

data_processing:
ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark) was used
Quantified signals were background corrected with Normexp method (offset value 10), normalized using the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm.

source_name: reference (pooled) sample

label_protocol: Total RNA (750 ng) from both the test and reference (pooled) samples were labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark)

growth_protocol: Animals were housed under standard conditions with free access to standard rodent chow and tap water ad libitum

extract_protocol: The mice were anticoagulated with 10 ml/kg (550 IU/mL) heparin , i.p. 2 min prior to cervical dislocation. The left kidney was removed, snap frozen in liquid nitrogen and stored at -80°C

treatment_protocol: LPS, prepared from E. coli 0111:B4 (Sigma-Aldrich, Budapest, Hungary), was suspended in sterile saline immediately before administration

value: NMRI

tag: gender

value: Male

value: kidney

source_name: test sample


title: L40_sucr_2d_repl2

description:
Series 2
Rep2
Rep2_sucr_2 day culture
CPM_TABLE_L40.txt


title: VIVO_WT_female_3

city: Isehara-shi

first: Atsushi

last: Fukuda

country: Japan

institute: Tokai University

data_processing:
Basecalls performed using bcl2fastq v2.17.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the Mouse reference genome (mm10) using TopHat 2.1.1 (bowtie2-2.2.3) with the option '-g 1 --no-mixed --no-discordant'.
NuDup ver.2.2 (NuGEN Technologies, San Carlos, CA) analyzing the redundancy of 8 bp molecular barcodes was used to remove PCR duplicate reads.
The read counts allocated for each gene and transcript (RefSeq Genes 2013.04.01) were quantified using a RPKM (Reads Per Kilo base per Million reads) method using StrandNGS 3.2 software (Agilent Technologies, Santa Clara, CA).
Genome_build: mm10
Supplementary_files_format_and_content: An excel format file (XLSX) includes RPKM quantification values and gene annotations of all samples.

source_name: Blastocyst

growth_protocol: For in vivo samples, embryonic day 2.5 embryos are flushed from uterus and they are cultured in KSOM medium until embyronic day 5. For in vitro samples, the zygote is generated by in vitro fertilization and cultured in KSOM until embryonic day 5.

extract_protocol:
Total RNA is extracted using Rneasy micro kit (Qiagen) with Dnase treatment.
Total RNA obtained from each sample was subjected to a sequencing library construction using Ovation Solo RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to the manufacture's protocol.

value: Female blastocyst derived from in vivo

tag: developmental stage

value: Embryonic day 5

value: BDF1 x C57BL/6


title: L40_sucr_14d_repl2

description:
Series 1
Rep2
Rep2_sucr_L40
Rep2_sucr_14 day culture
CPM_TABLE_14d_3lines.txt
CPM_TABLE_L40.txt


title: L40_UT_14d_repl2

description:
Series 1
Rep2
Rep2_ctr_L40
Rep2_ctr_14 day culture
CPM_TABLE_14d_3lines.txt
CPM_TABLE_L40.txt


title: VIVO_WT_female_2


title: VIVO_male_5

value: Male blastocyst derived from in vivo


title: 18: LPS 10 mg/kg 24h

description: Biological replicate 4 of 4. 10 mg/kg LPS, harvest at 24 hours


title: L40_UT_14d_repl3

description:
Series 1
Rep3
Rep3_ctr_L40
Rep3_ctr_14 day culture
CPM_TABLE_14d_3lines.txt
CPM_TABLE_L40.txt


title: SKM_iPSC2_Rep2

value: induced Pluripotent Stem Cell line, Oct4-GFP-positive


title: VIVO_male_2


title: 1: LPS 40 mg/kg 1.5h

description: Biological replicate 3 of 4. 40 mg/kg LPS, harvest at 1.5 hours


title: 12: vehicle

description: Equal volume of saline, harvest at 24 hours


title: 13: LPS 10 mg/kg 24h

description: Biological replicate 3 of 4. 10 mg/kg LPS, harvest at 24 hours


title: 35: vehicle

description: Equal volume of saline, harvest at 6 hours


title: SKM_iPSC2_Rep1


title: VIVO_male_1


title: L40_sucr_14d_repl1

description:
Series 1
Rep1
Rep1_sucr_L40
Rep1_sucr_14 day culture
CPM_TABLE_14d_3lines.txt
CPM_TABLE_L40.txt


title: 31: LPS 10 mg/kg 48h

description: Biological replicate 4 of 4. 10 mg/kg LPS, harvest at 48 hours


title: 28: LPS 10 mg/kg 48h

description: Biological replicate 3 of 4. 10 mg/kg LPS, harvest at 48 hours


title: L40_UT_14d_repl1

description:
Series 1
Rep1
Rep1_ctr_L40
Rep1_ctr_14 day culture
CPM_TABLE_14d_3lines.txt
CPM_TABLE_L40.txt


title: L37_sucr_14d_repl2

description:
Series 1
Rep2
Rep2_sucr_L37
CPM_TABLE_14d_3lines.txt


title: VIVO_KO_female_8

value: Female blastocyst derived from in vivo with Xist deletion


title: 19: LPS 10 mg/kg 24h

description: Biological replicate 2 of 4. 10 mg/kg LPS, harvest at 24 hours


title: 40: LPS 40 mg/kg 6h

description: Biological replicate 4 of 4. 40 mg/kg LPS, harvest at 6 hours


title: SKM_iPSC1_Rep2


title: SKM_iPSC1_Rep1


title: VIVO_KO_female_7


title: 9: LPS 40 mg/kg 1.5h

description: Biological replicate 2 of 4. 40 mg/kg LPS, harvest at 1.5 hours


title: VIVO_KO_female_6


title: L37_UT_14d_repl2

description:
Series 1
Rep2
Rep2_ctr_L37
CPM_TABLE_14d_3lines.txt


title: OSKM_iPSC2_Rep2


title: F1_sucr_14d_repl2

description:
Series 1
Rep2
Rep2_sucr_F1
CPM_TABLE_14d_3lines.txt


title: OSKM_iPSC2_Rep1


title: IVF_WT_female_4

value: Female blastocyst derived from in vitro


title: IVF_WT_female_2


title: OSKM_iPSC1_Rep2


title: 24: LPS 10 mg/kg 48h

description: Biological replicate 2 of 4. 10 mg/kg LPS, harvest at 48 hours


title: 14: LPS 10 mg/kg 24h

description: Biological replicate 1 of 4. 10 mg/kg LPS, harvest at 24 hours


title: 29: vehicle

description: Equal volume of saline, harvest at 48 hours


title: L37_sucr_14d_repl1

description:
Series 1
Rep1
Rep1_sucr_L37
CPM_TABLE_14d_3lines.txt


title: OSKM_iPSC1_Rep1


title: 11: LPS 40 mg/kg 1.5h

description: Biological replicate 1 of 4. 40 mg/kg LPS, harvest at 1.5 hours


title: IVF_male_6

value: Male blastocyst derived from in vitro


title: MEFs_Rep2

source_name: Mouse Embryonic Fibroblast

value: Mouse Embryonic Fibroblast


title: F1_UT_14d_repl2

description:
Series 1
Rep2
Rep2_ctr_F1
CPM_TABLE_14d_3lines.txt

value: fibroblast


title: IVF_WT_female_8


title: 34: LPS 40 mg/kg 6h

description: Biological replicate 3 of 4. 40 mg/kg LPS, harvest at 6 hours


title: 41: LPS 40 mg/kg 6h

description: Biological replicate 2 of 4. 40 mg/kg LPS, harvest at 6 hours


title: IVF_male_5


title: F1_UT_14d_repl1

description:
Series 1
Rep1
Rep1_ctr_F1
CPM_TABLE_14d_3lines.txt

value: 14 day culture


title: L37_UT_14d_repl1

description:
Series 1
Rep1
Rep1_ctr_L37
CPM_TABLE_14d_3lines.txt


title: F1_sucr_14d_repl1

description:
Series 1
Rep1
Rep1_sucr_F1
CPM_TABLE_14d_3lines.txt

value: sucrose


title: ESC_Rep2

value: Embryonic Stem Cell line, Oct4-GFP-positive


title: NHEM-c_co-cultured_with_A549_derived_exosomes_rep3

city: Louisville

first: Hongying

last: Hao

state: KY

address: 505 South Hancock Street

institute: University of Louisville

data_processing:
Illumina FastQ Generation version 1.0.0 used for basecalling.
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1). The FastQC results indicated that all sequences were of high quality (Q32).
Sequences were directly aligned to the Homo sapiens hg38 reference genome assembly (hg38.fa) using tophat2 (version 2.0.13) [6], generating alignment files in bam format.
Differentially expressed genes were identified for the four pairwise comparisons: A375EXO vs. Control, A549EXO vs. Control, A375EXO vs. A549EXO, A375EXO+A549EXO vs. Control using the tuxedo suite of programs including cuffdiff2 (version 2.2.1).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited cuffnorm normalized FPKM values

source_name: cell line

growth_protocol: NHEM-c cells were cultured in melanocyte growth medium M2 with supplement mix (PromoCell, Heidelberg, Germany) in a 5% CO2 incubator at 37C. A375 and A549 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% exosome-depleted fetal bovine serum (FBS) and penicillin (100 U/mL)/streptomycin (100 μg/mL). FBS was depleted of exosomes by ultracentrifugation at 100,000 x g for 18 h at 4C.

extract_protocol:
Total RNAs from cells were isolated using mirVana total RNA isolation kit (Life Technologies), according to the manufacturer’s guidelines. Total RNA was quantified using Nanodrop ND-1000 (Thermo Fisher Scientific). The integrity of these total RNAs was assessed using Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit- Set A (Cat# RS-122-2101) with poly-A enrichment.

treatment_protocol: A375 and A549 cell-derived exosomes were purified from cell culture supernatants by differential centrifugation.  Briefly, culture medium was collected and centrifuged at 400 x g for 10 min to remove whole cells. The supernatant was then centrifuged at 15,000 x g for 20 min to remove debris. This concentrated material was then ultracentrifuged at 100,000 x g for 90 min to generate the exosome pellet. The pellet was resuspended and washed twice with phosphate buffered saline (PBS). The quantity of the exosomes was determined using a Nanodrop ND-1000 spectrophotometer at 420 nm (Thermo Fisher Scientific, Pittsburgh, PA). NHEM-c cells were seeded in a 6-well plate. 250 ul of A375 or A549 cell-derived exosomes determined with an OD420 reading of 0.05 were added in each well twice (in the morning and in the afternoon) at the next day. Total RNAs from cells were isolated after 16 hours of adding tumor cell-derived exosomes.

value: NHEM-c

tag: exosomes

value: A549 cell-derived

tag: passages


title: NHEM-c_co-cultured_with_A549_derived_exosomes_rep2


title: ESC_Rep1


title: IVF_male_2

tag: strain


title: IVF_KO_female_8

tag: cell type

value: Female blastocyst derived from in vitro with Xist deletion


title: d9_SKM_Rep2


title: IVF_KO_female_4


title: NHEM-c_co-cultured_with_A549_derived_exosomes_rep1


title: 3: vehicle

description: Equal volume of saline, harvest at 1.5 hours

value: NMRI

value: Male

value: kidney


title: NHEM-c_co-cultured_with_A375_derived_exosomes_rep3

value: A375 cell-derived


title: d9_SKM_Rep1


title: 36: LPS 40 mg/kg 6h

description: Biological replicate 1 of 4. 40 mg/kg LPS, harvest at 6 hours


title: p6_recovery_24h_rep2

city: Katowice

first: Urszula

last: Korotko

address: Bankowa 12

country: Poland

institute: University of Silesia

data_processing:
Raw sequence reads were trimmed to remove poor quality calls using BBduk 35.02
Remaining sequences were mapped to the Arabidopsis TAIR10 genome using Bismark-0.20.0
Duplicated reads were removed, percentage methylation and read coverage at each site was determined by running the appropriate Bismark scripts (Bismark-0.20.0)
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: bedGraph files for each sample generated using Bismark-0.20.0

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Seeds of Arabidopsis thaliana ecotype Columbia were sown on Jiffy pots (Jiffy, Moerdijk, Netherlands) and stratified in the darkness at 4 °C for 48 h. After stratification, seeds were transferred to the growth chamber (16 h photoperiod, photosynthetic photon flux density (PPFD) of 100 µmol m⁻2s⁻1 and temperature 21 °C) and regularly watered.

extract_protocol:
Genomic DNA was extracted using the micro C-TAB procedure. The purity of the DNA samples was determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Waltham, USA), whereas the integrity was evaluated using agarose gel electrophoresis. An exact estimation of genomic DNA concentration was conducted using fluorimetry with dsDNA specific dye and QuantiFluor Single Tube Fluorometer instrument (Promega, Madison, USA).
One µg of genomic DNA was fragmented in 50 µl of 0.5x Tris-EDTA buffer using Bioruptor Plus sonication device (Diagenode, Liège, Belgium) under ten cycles of 30 s ON and 90 s OFF power conditions. Then, fragmented DNA was purified with 1.8x Agencourt AMPure XP (Beckman Coulter, Brea, USA) and eluted in 40 µl of ddH2O. Whole genome bisulfite sequencing libraries were prepared using the NEXTflex Bisulfite-Seq Kit (BIOO Scientific, Austin, USA) according to the manufacturer’s instructions with minor changes. Briefly, genomic DNA fragments were subjected to end repair, clean-up and adenylation. Next, barcoded adapters were ligated. The ligation products were purified and size-selected with Agencourt AMPure XP (Beckman Coulter, Brea, USA). Prepared adapter-ligated fragments were subjected to bisulfite conversion with the EZ DNA Methylation-Lightning Kit (Zymo Research, Irvine, USA) according to manufacturer's protocol, and eluted in 17 µl of M-Elution buffer. Five µl of converted DNA was amplified in 50 µl volume of PCR reaction. Amplicons were purified twice with Agencourt AMPure XP (Beckman Coulter, Brea, USA).

treatment_protocol: 21-day old seedlings were subjected to heat stress (42 °C) for 24 h. Fourth, fifth and sixth leaves from control plants were collected just before temperature increase, while leaves from treated plants were harvested in 3 time points - after: 6, 12 and 24 h. During stress treatment plants were not watered. After 24 h of heat stress, standard temperature conditions were restored together with watering. Leaves from recovering plants were collected after another 6, 12 and 24 h. The tissue samples were frozen immediately in liquid nitrogen and stored at −80 °C until DNA isolation.

tag: ecotype

value: Columbia

value: recovery 24h

tag: replicates


title: NHEM-c_co-cultured_with_A375_derived_exosomes_rep2


title: d9_OSKM_Rep2


title: p6_recovery_24h_rep3


title: 22: LPS 10 mg/kg 48h

description: Biological replicate 1 of 4. 10 mg/kg LPS, harvest at 48 hours

tag: tissue


title: d9_OSKM_Rep1


title: NHEM-c_co-cultured_with_A375_derived_exosomes_rep1


title: d6_SKM_Rep2


title: NHEM-c_without_exosomes_control_rep2


title: p6_recovery_24h_rep1


title: p5_recovery_12h_rep3

value: recovery 12h


title: p5_recovery_12h_rep2


title: LPS_2_hi

city: Stanford

first: Julia

last: Marschallinger

address: 1201 Welch Road

department: Neurology

institute: Stanford University

description: BODIPY-high microglia (lipid-droplet rich)

data_processing:
Sequencing of isolated microglia was carried out with Novaseq 6000, paired end, 2x 100 bp depth sequencer.
The quality of fastq files was assessed using FASTQC (v 0.11.4).
Reads were mapped to mouse mm9 reference genome using STAR (v 2.5.3a).
Raw read counts were generated with STAR using the GeneCounts function.
Differential expression analysis was performed using DESeq2 with standard settings.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

extract_protocol:
Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol.
cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina).

tag: age

value: 3 month old

tag: Sex

value: male


title: LPS_1_hi


title: NHEM-c_without_exosomes_control_rep3

tag: cell line


title: p5_recovery_12h_rep1

tag: treatment


title: d6_SKM_Rep1


title: NHEM-c_without_exosomes_control_rep1


title: IVF_KO_female_3

value: Embryonic day 5

value: BDF1 x C57BL/6


title: d6_OSKM_Rep2


title: LPS_3_hi


title: p4_recovery_6h_rep3

value: recovery 6h


title: p4_recovery_6h_rep2


title: LPS_1_lo

description: BODIPY-low microglia (lipid-droplet low)


title: d4_SKM_Rep2


title: Mouse palatal mesenchyme rep3

city: Iowa City

last: Cornell

state: Iowa

address: 1-400 D Bowen Science Bldg. 51 Newton Road

department: Anatomy and Cell Biology

institute: University of Iowa

data_processing:
Sequencing reads were trimmed with Trimmomatic (0.38) using NexteraPE sequences.
Trimmed paired reads were mapped with Bowtie2 (default parameters). Sorting, removal of PCR duplicates and conversion from SAM to BAM files were performed using SAMtools
We employed DeepTools (v 2.0) to check the reproducibility of the biological replicates and generate bigWig coverage files for visualization
Peaks were called using MACS2 (v2.1.1) (parameter: --nomodel --nolambda --gsize 2.7e9 --keep-dup all --slocal 10000 ).
Genome_build: mm10
Supplementary_files_format_and_content: bw, peaks bed

source_name: Mesenchymal cells from palatal shelves

extract_protocol:
Isolated cells were lysed with 50 µL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40; all components purchased from Sigma) in a centrifuge at 500 x g for 15 minutes at 4°C.
Pelleted nuclei were resuspended in 50 µL tagmentation reaction mix (25 µL Nextera TD Buffer, 2.5 µL Nextera TD Enzyme, and 22.5 µL H2O, all from the Nextera DNA Sample Preparation Kit (Illumina). Immediately after Tn5 tagmentation, DNA samples were purified and indexed using NEBNext® High-Fidelity 2x PCR Master Mix (New England Biolabs) with a customized Nextera PCR primer pair, according to the following program: 72°C for 5 minutes; 98°C for 30 seconds; 11 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute; and hold at 4°C. All DNA libraries that exhibited a nucleosome pattern in the BioAnalyzer 2100 Assay passed the pre-sequencing QC process and were pooled for high-throughput sequencing.

treatment_protocol: For each biological replicate, five palatal shelves from E14.5 mouse embryos were digested with 0.25% trypsin-EDTA (Life Technologies) at 4°C for 10 minutes, after which the reaction was stopped using trypsin Inhibitor (Life Technologies). Under a dissecting microscope, the epithelium was isolated for ATAC-seq by gently peeling using microforceps. The remaining tissue, comprised largely of mesenchymal cells, was also collected for control samples. Tissues were disassociated with trypsin-EDTA.

value: mesenchyme


title: Mouse palatal mesenchyme rep2


title: LPS_3_lo


title: p3_heat_stress_24h_rep3

value: heat stress 24h


title: Mouse palatal mesenchyme rep1


title: p3_heat_stress_24h_rep2


title: d4_OSKM_Rep2

source_name: Reprogramming intermediates


title: d4_OSKM_Rep1


title: VIVO_male_4

value: Male blastocyst derived from in vivo


title: LPS_2_lo


title: HK_p2

city: Suwon

first: Hamid

last: Iqbal

address: 2066 Seoburo, Jangan-gu Suwon

department: Pharmacy

institute: Sungkyunkwan University

description: Preventive effect of ∆pep27 and underlying mechanism involved in inhibiting ulcerative colitis using dextran sulfate sodium (DSS) in mice is investigted.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: Biotin

source_name: HK

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Mice immunized with ∆pep27 were treated with  dextran sulfate sodium (DSS) around 7 to 9 days and evaluated for inflammatory pathways

extract_protocol: Total RNA was extracted with Triazole according to the manufaacturer instruction.

treatment_protocol: ∆pep27 was administered intranasally 3 times once a week followed by dextran sulfate sodium (DSS) in mice to investigae gene expression level.

value: Inflammatory colon


title: d6_OSKM_Rep1


title: Mouse palatal epithelium rep3

source_name: Epithelial cells from palatal shelves

value: epithelium


title: HK_p1


title: p3_heat_stress_24h_rep1


title: p2_heat_stress_12h_rep3

value: heat stress 12h


title: d2_SKM_Rep2


title: Mouse palatal epithelium rep2


title: d4_SKM_Rep1


title: Mouse palatal epithelium rep1


title: p4_recovery_6h_rep1


title: PEP3_DSS_p1


title: d2_OSKM_Rep2


title: d2_SKM_Rep1


title: PEP2_DSS_p2


title: p2_heat_stress_12h_rep2


title: PEP2_DSS_p1


title: PEP1_DSS_p2


title: p2_heat_stress_12h_rep1


title: p1_heat_stress_6h_rep3

value: heat stress 6h


title: d2_OSKM_Rep1


title: PEP3_DSS_p2


title: p1_heat_stress_6h_rep2


title: PEP1_DSS_p1


title: 200 mg/L AP-3 for 48 h

city: Shenzhen

first: Xinran

last: Wang

state: Guangdong

address: No.1068 Xueyuan Avenue

department: Center for Synthetic Biochemistry

country: China

institute: Shenzhen Institute of Advanced Technology, Chinese Acadamy of Science

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the  Actinosynnema pretiosum ATCC 31280 genome assembly using bowtie2（version: 2-2.0.5）.
Gene abundance measurements were generationed and normalized  using BEDTools（version:2.16.1） ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Genome_build: Actinosynnema pretiosum ATCC 31280 (CP029607) ASM351620v1
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values for each Sample

organism: Actinosynnema pretiosum

source_name: bacteria

growth_protocol: For fermentation, the first seed medium (3.0% tryptone soya broth powder, 0.5% yeast extract, and 5.0% sucrose (w/v), pH 7.5) was inoculated with agar-grown mycelia and cultivated at 30 °C, 220 rpm for 24 h. Subsequently, the second seed medium (3.0% tryptone soya broth powder, 0.5% yeast extract and 2.5% sucrose, 1.0% soluble starch (w/v), 0.05% isobutanol, and 0.05% isopropanol (v/v), pH 7.5) was inoculated with 1 mL of the first seed culture, incubated for another 24 h at 30 °C. Fermentation medium (yeast extract 0.8%, malt extract 1.0%, sucrose 1.5%, soluble starch 2.5% (w/v), isobutanol 0.5% and isopropanol 1.2% (v/v), pH 7.5) was inoculated with the second seed culture at 10% (v/v) and incubated at 25 °C and 220 rpm for 7 days

extract_protocol:
One mililiter culture was collected during fermentation process. The total RNA was extracted with Redzol reagent according to the procedures recommended by the manufacturer (SBS Genetech, China). Total DNA was removed by DNase I (Thermo Fisher, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wildtype

tag: agent


title: 200 mg/L AP-3 for 72 h


title: DSS_p2

source_name: DSS


title: 200 mg/L AP-3


title: p0_control_rep3

value: control


title: 100 mg/L AP-3


title: p0_control_rep2

value: Columbia


title: the fifth largest follicle (F5) rep5

city: Chongqing

first: Gao

last: Guangliang

address: Street Address, No. 51 Changlong Avenue Rongchang County

institute: Chongqing Academy of Animal Sciences

description:
domestic goose
5HPGF5

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of six strand-specific libraries were mapped to the pig reference genome (Suscrofa.10.2 from Ensemble) with TopHat (v.2.1.0)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Cufflinks (v.2.2.1).
Cuffquant (part of Cufflinks) was used to generate abundance files, which were applied to Cuffdiff (part of Cufflinks) to detect DE mRNAs/genes between the two groups.
Transcripts were assembled by Stringtie version 1.2.2.
AssemblyLine (http://assemblyline.googlecode.com) was used to characterize and filter background noise and to perform meta-assembly by merging the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
To obtain genomic characterizations for all identified lncRNA transcripts, we ran FEELnc_classifier.pl (a Perl script in FEELnc).
Genome_build: Goose
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample.

organism: Anser cygnoides

source_name: goose granulosa cells

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: development stage

value: goose granulosa cells

value: 40 Week


title: p1_heat_stress_6h_rep1


title: 50 mg/L AP-3

tag: time


title: rad53-1 pol3-01 +HU 45min BrdU-IP-ssSeq

first: zhiguo

last: zhang

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

data_processing:
Reads were aligned to the yeast genome (sacCer3) using the Bowtie2 software. Only the consist pair reads were used for the further analysis.
The genome-wide reads coverage of Watson and Crick strand was calculated by BEDTools and  in-house Perl  programs.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: For G1 cell synchronization, alpha factor was added at cell density OD600=0.4-0.5 to finial concentration at 5ug/ml for wild type Bar1 and 50ng/ml for bar1 mutants.  After 3hr arrest at 30°C, the cell was released to fresh YPD medium with or without 200mM hydroxyurea.

extract_protocol:
the collected samples were incubated with 1% fresh-made formaldehyde at 25°C for 20mins, and quenched with 0.125M Glysine for 5mins.  The harvested cells were lysed with glass beads, and the chromatin pellet were washed and sonicated. The average DNA fragment size is about 200-400bp.  Sheared chromatin was immunoprecipitated with an protein-specific antibody. The chromatin was reverse-cross-linked and immunoprecipitated.  DNA was exacted with the Chelex-100 method
ssDNA library preparation method was modified from previous one (Meyer et al., 2012). To preserve the strand information, we use a specific RNA ligase, which also can ligated the ssDNAs in a sequence-independent way. The ssDNA library strand information was kept by sequential 3’ end and  5’ end ligation.

tag: media

value: YPD+HU

tag: cell cycle stage

value: S

tag: chip antibody

value: Anti-BrdU (BD BioScience, 347580)


title: rad53-1 pol2-04 +HU 45min BrdU-IP-ssSeq


title: p0_control_rep1


title: ΔlytSR versus WT strain after 8h of culture replicat 3

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

hyb_protocol: cRNA was co-hybridized on the microarray

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters and data were extracted after Linear-Lowess normalisation.  Genes with significant different expression (P0.05) were selected based on at least a 2 fold change in expression level.

organism: Staphylococcus lugdunensis

source_name: cells

label_protocol: cRNA was labelled with either Cy3 or Cy5

growth_protocol: S. lugdunensis strains were grown in trypticase soy broth (TSB) at 37°C under shaking (150 rpm), and cells were collected at 6 and 8 h of growth.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) following the manufacturer’s procedure. Two DNase treatments were successively performed using DNase I (Sigma-Aldrich) and Turbo DNA free (Thermo Fisher Scientific). Quality of RNA was evaluated using the RNA 6000 Nano with a Bioanalyzer (Agilent, Les Ulis, France).

value: [delta]lytSR

tag: time point

value: 8h of culture

value: Wild-Type


title: ΔlytSR versus WT strain after 8h of culture replicat 2

tag: strain


title: DSS_p1


title: AC_Mock

city: Tianjin

first: feiyu

last: fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

department: Key Laboratory of Systems Microbial Biotechnology

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences.

description: RNA sample prepared as the following description: Germinated young mycelia of A. coerulea after 22-24 pre-culture in PDB medium were harvested and transferred into a new 30 ml potassium phosphate buffer supplement with an equal volume of N, N-dimethylformamide as mock. Additional two-hour cultivations were performed to induction of the 11β-hydroxylase gene expression.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the clean reads were used to create a  de novo transcriptome assembly using the Trinity pipeline (v2.4.0)
The abundance for each of the resulted transcripts was calculated by RSEM (v1.2.0) using the Fragments Per Kilobase per Million (FPKM) measure
Detailed parameters for de novo trscripts assambly using Trinity: perl ../trinityrnaseq-Trinity-v2.4.0/Trinity --seqType fq --max_memory 50G --left AC_RSA_1.fq --right AC_RSA_2.fq --trimmomatic --full_cleanup
Detailed parameters for abundance measurements: perl ../trinityrnaseq-Trinity-v2.4.0/util/align_and_estimate_abundance.pl --transcripts ./AC.Trinity.fasta --seqType fq --left AC_RSA_1.fq --right AC_RSA_2.fq --prep_reference --est_method RSEM --thread_count 8 --aln_method bowtie2 --output_dir ./AC_RSA_res
Supplementary_files_format_and_content: Tab-delimited RSEM results include FPKM values for each Sample .

organism: Absidia caerulea

source_name: Mycelia of wild-type A. coerulea

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelia

value: Equal volume of N, N-dimethylformamide


title: ΔlytSR versus WT strain after 6h of culture replicat 2

value: 6h of culture


title: ΔlytSR versus WT strain after 6h of culture replicat 1


title: 0 AP-3


title: IEC_7

status: Public on Nov 05 2019

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
Quality Control of sequenced samples was performed by FASTQC software
Reads were mapped against the mouse (mm10) reference genome by Tophat [2] program to account for spliced junctions.
The resulting BAM alignment files for the samples were transformed into a table of raw counts via the summarize Overlaps function (in Union mode) from the GenomicAlignments bioconductoR package
Resulting table of counts was used as input for the Differential Expression (DE) analysis, carried out by  DESeq2, to account for differentially expressed genes among the different conditions
GO enrichment was tested using PantherDB webserver resources.
Genome_build: mm10 mouse reference genome
Supplementary_files_format_and_content: DESeq2 normalized table of counts in tab separated plain text format.

source_name: Nr3c1IEC-/-_Enriched Colonic Epithelial Cells

growth_protocol: Enrichment of mouse colonic epithelial cells using Percoll gradient (no culture)

extract_protocol:
RNeasy Mini Kit - QIAGEN
TruSeq RNA Sample Preparation v2 (Illumina Inc.)
Non-stranded mRNAlibrary

treatment_protocol: Intraperitoneal injection of Tamoxifen 5 consecutive days.  The colonic epithelial cells were obtained 7 days after the first Tamoxifen administration

tag: strain background

tag: genotype/variation

value: B6-Cg-Nr3c1-Vil-Cre/ERT2 (Nr3c1IEC-/-)

tag: cell type

value: Enriched Colonic Epithelial Cells


title: IEC_6

source_name: WT_Enriched Colonic Epithelial Cells

value: wild type


title: Control_p2

source_name: Control

tag: tissue

value: Non-inflammatory colon


title: IEC_12


title: ΔlytSR versus WT strain after 8h of culture replicat 1


title: ΔlytSR versus WT strain after 6h of culture replicat 3


title: Control_p1


title: IEC_5


title: IEC_3


title: IEC_8


title: AC_RSA

description: RNA sample prepared as the following description: Germinated young mycelia of A. coerulea after 22-24 pre-culture in PDB medium were harvested and transferred into a new 30 ml potassium phosphate buffer supplement with 170 mg/L RSA dissolved in N, N-dimethylformamide. Additional two-hour cultivations were performed to induction of the 11β-hydroxylase gene expression.

value: 170 mg/L 11-deoxycortisol 21-acetate (RSA) dissolved in N, N-dimethylformamide


title: adult_VGlut_Dam-POLII_1: RNA Pol II occupancy in adult glutamatergic neurons

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Library strategy: DamID-seq
The forward sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 (see PMID: 26112292 for details of the damidseq_pipeline)
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded, followed by quantile normalisation and pseudocount addition.
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 normalised fold changes between the experimental and Dam-only control as a gff file produced by the damidseq_pipeline

organism: Drosophila melanogaster

source_name: adult heads (3-5 days old)

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the Illumina Truseq Library Kit

treatment_protocol: Animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction

tag: expressed transgene

value: Dam-RNA polymerase II

tag: cell type being profiled

value: glutamatergic neurons

tag: developmental stage

value: 3-5 day old adults


title: adult_Gad1_Dam-POLII_3: RNA Pol II occupancy in adult GABAergic neurons

value: GABAergic neurons


title: adult_Ets65A-RA_Dam-Ets65A-RA_2: Ets65A-RA binding in Ets65A-RA expressing neurons in adult heads

value: Ets65A-RA expressing neurons


title: adult_VGlut_Dam-POLII_3: RNA Pol II occupancy in adult glutamatergic neurons


title: adult_acj6_Dam-acj6_1: acj6 binding in acj6 expressing neurons in adult heads

value: acj6 expressing neurons


title: adult_Gad1_Dam-POLII_1: RNA Pol II occupancy in adult GABAergic neurons


title: adult_acj6_Dam-acj6_2: acj6 binding in acj6 expressing neurons in adult heads


title: adult_VGlut_Dam-POLII_2: RNA Pol II occupancy in adult glutamatergic neurons


title: adult_Ets65A-RA_Dam-Ets65A-RA_1: Ets65A-RA binding in Ets65A-RA expressing neurons in adult heads


title: adult_Gad1_Dam-POLII_2: RNA Pol II occupancy in adult GABAergic neurons


title: CR4

city: Gyeonggi-do

first: Hyonchol

last: Jang

address: 323, Ilsan-ro, Ilsandong-gu, Goyang-si

institute: National Cancer Center

data_processing:
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using TopHat 2.1.1 in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The relative transcript abundances were
measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Clone of R-H460 cells surviving after cisplatin treatment

extract_protocol:
RNAs were extracted from the Lung of Homo Sapiens. Poly(A) mRNA using the Illumina  TruSeq RNA Sample Prep Kit v2, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

value: Lung


title: CR3


title: R-H460

source_name: Reprogrammed Lung cancer cell with introduction of yamanaka factors


title: H460

source_name: Lung cancer parent cell


title: CR1


title: L3_VGlut_Dam-POLII_2: RNA Pol II occupancy in larval glutamatergic neurons

source_name: Partially dissected anterior half of 3rd instar larvae (containing CNS but no gut tissue

value: 3rd instar larvae


title: L3_VGlut_Dam-POLII_1: RNA Pol II occupancy in larval glutamatergic neurons


title: L3_VGlut_Dam-POLII_3: RNA Pol II occupancy in larval glutamatergic neurons


title: L3_Gad1_Dam-POLII_3: RNA Pol II occupancy in larval GABAergic neurons


title: CR2


title: adult_ChAT_Dam-POLII_1: RNA Pol II occupancy in adult cholinergic neurons

value: cholinergic neurons


title: L3_Gad1_Dam-POLII_1: RNA Pol II occupancy in larval GABAergic neurons


title: adult_ChAT_Dam-POLII_2: RNA Pol II occupancy in adult cholinergic neurons


title: L3_ChAT_Dam-POLII_3: RNA Pol II occupancy in larval cholinergic neurons


title: L3_Gad1_Dam-POLII_2: RNA Pol II occupancy in larval GABAergic neurons


title: L3_ChAT_Dam-POLII_2: RNA Pol II occupancy in larval cholinergic neurons


title: L3_ChAT_Dam-POLII_1: RNA Pol II occupancy in larval cholinergic neurons


title: emb_VGlut_Dam-POLII_3: RNA Pol II occupancy in embryonic glutamatergic neurons

source_name: whole, newly hatched 1st instar larvae

value: embryo


title: mdR-H460

source_name: Differentiated R-H460 cells


title: adult_ChAT_Dam-POLII_3: RNA Pol II occupancy in adult cholinergic neurons


title: emb_Gad1_Dam-POLII_1: RNA Pol II occupancy in embryonic GABAergic neurons


title: emb_VGlut_Dam-POLII_2: RNA Pol II occupancy in embryonic glutamatergic neurons


title: emb_ChAT_Dam-POLII_2: RNA Pol II occupancy in embryonic cholinergic neurons


title: emb_ChAT_Dam-POLII_1: RNA Pol II occupancy in embryonic cholinergic neurons


title: 18-0648_BOLD74_Admit

city: Columbus

first: Benjamin

middle: T.

last: Kopp

state: Ohio

address: 700 Children’s Drive

department: Section of Pediatric Pulmonology

institute: Nationwide Children’s Hospital

data_processing:
Each sample was aligned to the GRCh38.p9 assembly of the Homo Sapiens reference from NCBI (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.35/) using version 2.6.0c of the RNA-Seq aligner STAR
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count
Differentially expressed features were calculated using DESeq2
Genome_build: human NCBI GRCh38.p9
Supplementary_files_format_and_content: Excel spreadsheet containing normalized read counts for each sample (columns U - BU) and differential expression data (columns G - P) for each feature

source_name: whole blood

extract_protocol:
rRNA was removed from 350 ng using Illumina’s Ribo-Zero Globin kit (Illumina, CA)
libraries were constructed from first strand cDNA using Illumina’s TruSeq Stranded Total RNA Library kit (Illumina, CA)

tag: subject id

value: whole blood

tag: patient diagnosis

value: sickle cell disease (SCD)

tag: condition

value: VOC


title: 18-0645_BOLD64_ACS

value: ACS


title: 18-0643_BOLD70_Baseline

value: Baseline


title: emb_ChAT_Dam-POLII_3: RNA Pol II occupancy in embryonic cholinergic neurons


title: emb_Gad1_Dam-POLII_3: RNA Pol II occupancy in embryonic GABAergic neurons


title: 18-0641_BOLD62_Baseline


title: 18-0631_BOLD05_Baseline


title: 18-0468_BOLD71_Admit


title: 18-0630_BOLD64_Baseline


title: 18-0467_BOLD70_ACS


title: 18-0647_BOLD32_Admit


title: 18-0466_BOLD67_Admit


title: 18-0463_BOLD59_Admit


title: 18-0462_BOLD54_ACS


title: 18-0464_BOLD62_ACS


title: 18-0458_BOLD25_ACS


title: 18-0459_BOLD28_ACS


title: 18-0460_BOLD29_Admit


title: 18-0457_BOLD21_Admit


title: emb_Gad1_Dam-POLII_2: RNA Pol II occupancy in embryonic GABAergic neurons


title: 18-0637_BOLD28_Baseline


title: 18-0469_BOLD86_ACS


title: 18-0456_BOLD18_Admit


title: 18-0454_BOLD15_Admit


title: 18-0465_BOLD63_ACS


title: 18-0629_BOLD01_Baseline


title: 18-0450_BOLD01_Admit


title: 18-0445_BOLD59_Baseline


title: 18-0455_BOLD16_ACS


title: 18-0444_BOLD54_Baseline


title: 18-0439_BOLD21_Baseline


title: emb_VGlut_Dam-POLII_1: RNA Pol II occupancy in embryonic glutamatergic neurons


title: 18-0452_BOLD07_ACS


title: 18-0451_BOLD02_ACS


title: 18-0437_BOLD16_Baseline


title: 18-0436_BOLD15_Baseline


title: GAR1473

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm10 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes we used HTseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tsv files contain raw read count; they have two columns where the first column specifies the gene name and the second the actual read count

source_name: liver

extract_protocol:
Total RNA was extracted from inguinal WAT, BAT, liver and muscle using Qiazol according to the manufacturer’s instructions (Qiazol Lysis Reagent, QIAGEN). The quality of the RNA was determined with the Agilent 2100 BioAnalyzer (RNA 6000 Nano Kit, Agilent). All samples had a RNA integrity number (RIN) value greater than .8
For library preparation, 1 µg of total RNA per sample was used. RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).
Strand-specific RNA libraries were sequenced as 100 bp paired-end runs on an Illumina HiSeq4000 platform.

value: liver

tag: genotype

value: FGF21 KO

tag: gender

value: male


title: GAR1474


title: GAR1472


title: GAR1469

value: UCP1/FGF12 double KO


title: GAR1468


title: GAR1470


title: GAR1467


title: GAR1466


title: GAR1465


title: GAR1462

value: UCP1 KO


title: GAR1463


title: GAR1461


title: GAR1464


title: GAR1459

value: WT


title: GAR1460


title: GAR1457


title: GAR1471


title: GAR1458


title: GAR1451

source_name: muscle

value: muscle


title: GAR1450


title: GAR1453


title: GAR1454


title: GAR1455


title: GAR1449


title: GAR1452


title: GAR1447


title: GAR1446


title: GAR1444


title: GAR1448


title: GAR1443


title: GAR1442


title: GAR1439


title: GAR1440


title: GAR1441


title: GAR1438


title: GAR1437


title: GAR1436


title: GAR1435


title: Microglia, H9-p2-431_Male_Dicer_KO_PS19

city: San Francisco

first: Lay

last: Kodama

address: 1650 Owens St.

department: Gladstone Institute of Neurological Disease

institute: University of California San Francisco

description: mRNA expression in microglia

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trim the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (tsv) containing 721 samples and mapped gene counts.

source_name: FACS isolated adult microglia

extract_protocol:
In online methods
Smart-Seq2 protocol (in online methods)

value: brain

tag: age

value: 9 months

tag: Sex

value: Male

tag: gate


title: Microglia, H8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia

value: Female


title: Microglia, H9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H7-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: GAR1456


title: Microglia, H7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: GAR1445


title: Microglia, H7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: 18-0746_BOLD07_Baseline


title: Microglia, H5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H11-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, H1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G7-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G4-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G3-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G2-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G12-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G11-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G10-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G1-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, G5-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p1-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p1-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p1-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F6-p2-426_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F9-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F8-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F7-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p2-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p2-421_Female_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p1-431_Male_Dicer_KO_PS19

description: mRNA expression in microglia


title: Microglia, F5-p2-419_Female_Dicer_KO_PS19

description: mRNA expression in microglia